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2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE)最新文献

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[Regular Paper] Inference of Genetic Networks Using Random Forests: Use of Different Weights for Time-Series and Static Gene Expression Data 使用随机森林的遗传网络推断:对时间序列和静态基因表达数据使用不同权重
Shuhei Kimura, M. Tokuhisa, Mariko Okada
Genetic network inference methods using random forests have shown promise. Some of the random-forest-based inference methods have an ability to analyze both time-series and static gene expression data. We think however that, as the gene expression levels at two adjacent measurements of a time-series data are often similar to each other, the gene expression levels at each measurement in the time-series data are less informative than those in the static data. On the basis of this idea, we proposed a new inference method that relies more on static gene expression data than time-series ones. Through the numerical experiments, we showed that the quality of the inferred genetic network is slightly improved by giving greater importance to static data than time-series ones. Although we develop the new method by modifying the random-forest-based inference method proposed by the authors, we could introduce the idea in this study into any inference method that is capable of analyzing both time-series and static gene expression data.
利用随机森林的遗传网络推理方法已显示出良好的前景。一些基于随机森林的推理方法具有分析时间序列和静态基因表达数据的能力。然而,我们认为,由于时间序列数据的两个相邻测量值的基因表达水平通常彼此相似,因此时间序列数据中每个测量值的基因表达水平比静态数据中的基因表达水平提供的信息要少。在此基础上,我们提出了一种新的推理方法,该方法更多地依赖于静态基因表达数据而不是时间序列数据。通过数值实验,我们表明,通过对静态数据的重视程度高于对时间序列数据的重视程度,推导出的遗传网络的质量略有提高。虽然我们通过修改作者提出的基于随机森林的推理方法来开发新方法,但我们可以将本研究中的思想引入任何能够分析时间序列和静态基因表达数据的推理方法中。
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引用次数: 1
Title Page i 第1页
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引用次数: 0
[Regular Paper] Biomedical Data Acquisition and Processing to Recognize Emotions for Affective Learning [常规论文]生物医学数据采集与处理:情感学习的情感识别
A. Grünewald, David Kroenert, Jonas Poehler, R. Brück, Frédéric Li, Julian Littau, Katrin Schnieber, A. Piet, M. Grzegorzek, Henrik Kampling, Björn Niehaves
Emotion recognition is a increasingly popular topic because of its potential applications in the field of affective learning. It allows the development of systems able to adapt themselves to the users' emotional state to improve the learner's experience and learning. In this paper, we introduce a new biomedical multi-sensor platform for realtime acquisition of physiological data comprising Temperature, Electroencephalography (EEG), Electroocculography (EOG), Galvanic Skin Response (GSR), Heart Rate and Blood Oxygen Saturation. We describe experimental scenarios for the induction of emotions relevant in a context of affective learning (happiness, frustration, boredom) to build a set of emotionrelated data. We carry out a basic classification study by computing hand-crafted features on the time and frequency domains of signals, and training a Support-Vector-Machine (SVM) classifier to demonstrate the feasibility of our approach.
情绪识别由于其在情感学习领域的潜在应用而成为一个越来越受欢迎的话题。它允许开发能够适应用户情绪状态的系统,以改善学习者的体验和学习。在本文中,我们介绍了一个新的生物医学多传感器平台,用于实时采集生理数据,包括体温、脑电图(EEG)、脑电(EOG)、皮肤电反应(GSR)、心率和血氧饱和度。我们描述了情感学习背景下相关情绪诱导的实验场景(快乐、沮丧、无聊),以建立一套情感相关数据。我们通过在信号的时域和频域上计算手工制作的特征来进行基本的分类研究,并训练支持向量机(SVM)分类器来证明我们方法的可行性。
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引用次数: 10
Study on the Channel Characteristics of Auxiliary Medical Devices Based on MDAPSK Technology 基于MDAPSK技术的辅助医疗器械通道特性研究
Xueping Li, Yuan Yu, N. Yu
According to the communication channel differences, auxiliary medical devices can be divided into wearable medical devices and implantable medical devices. For wearable medical devices, the channel error rate is analyzed by analogy method. It is found that the logarithmic distribution model is more consistent with the actual situation. Then, based on the analyzing of error generation mechanism, the formula for calculating error rate of implantable medical devices is obtained. The accuracy of the formula is verified by the comparison of simulation and experiment. The biological channel error rate of auxiliary medical devices is analyzed in this paper, which provide a theoretical reference for auxiliary medical devices' clinical application.
根据通信渠道的不同,辅助医疗器械可分为可穿戴医疗器械和植入式医疗器械。针对可穿戴医疗设备,采用类比法分析了信道误差率。研究发现,对数分布模型更符合实际情况。然后,在分析误差产生机理的基础上,得到了植入式医疗器械误差率的计算公式。通过仿真与实验对比,验证了公式的准确性。分析了辅助医疗器械的生物通道误差率,为辅助医疗器械的临床应用提供理论参考。
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引用次数: 0
Comparison of Region of Interest Segmentation Methods for Video-Based Heart Rate Measurements 基于视频心率测量的兴趣区域分割方法比较
Peixi Li, Y. Benezeth, Keisuke Nakamura, R. Gomez, Chao Li, Fan Yang
Conventional contact photoplethysmography (PPG) sensors are not suitable in situations of skin damage or when unconstrained movement is required. As a consequence, remote photoplethysmography (rPPG) has recently emerged because it provides remote physiological measurements without expensive hardware and improves comfort for long term monitoring. RPPG estimation methods use the spatially averaged RGB values of pixels in a Region Of Interest (ROI) to generate a temporal RGB signal. The selection of ROI is a critical first step to obtain reliable pulse signals and must contain as many skin pixels as possible with a low percentage of non-skin pixels. In this paper, we experimentally compare seven ROI segmentation methods in the perspective of heart rate (HR) measurements with dedicated metrics. The algorithms are compared using our in-house database UBFC-RPPG, comprising of 53 videos specifically geared towards rPPG analysis.
传统的接触式光电容积脉搏波传感器不适用于皮肤损伤或需要自由运动的情况。因此,远程光电容积脉搏图(rPPG)最近出现了,因为它提供了远程生理测量,而不需要昂贵的硬件,并且提高了长期监测的舒适性。RPPG估计方法使用感兴趣区域(ROI)中像素的空间平均RGB值来生成时间RGB信号。ROI的选择是获得可靠脉冲信号的关键第一步,必须包含尽可能多的皮肤像素和低百分比的非皮肤像素。在本文中,我们实验比较了7种ROI分割方法在心率(HR)测量与专用指标的角度。使用我们的内部数据库UBFC-RPPG对算法进行比较,该数据库包含53个专门针对rPPG分析的视频。
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引用次数: 8
RLALIGN: A Reinforcement Learning Approach for Multiple Sequence Alignment RLALIGN:多序列对齐的强化学习方法
R. Ramakrishnan, Jaspal Singh, M. Blanchette
Multiple sequence alignment (MSA) is one of the best studied problems in bioinformatics because of the broad set of genomics, proteomics, and evolutionary analyses that rely on it. Yet the problem is NP-hard and existing heuristics are imperfect. Reinforcement learning (RL) techniques have emerged recently as a potential solution to a wide diversity of computational problems, but have yet to be applied to MSA. In this paper, we describe RLALIGN, a method to solve the MSA problem using RL. RLALIGN is based on Asynchronous Advantage Actor Critic (A3C), a cutting-edge RL framework. Due to the absence of a goal state, however, it required several important modifications. RLALIGN can be trained to accurately align moderate-length sequences, and various heuristics allow it to scale to longer sequences. The accuracy of the alignments produced is on par with, and often better than those of well established alignment algorithms. Overall, our work demonstrates the potential of RL approaches for complex combinatorial problems such as MSA. RLALIGN will prove useful for realignment tasks, where portions of a larger alignment need to be optimized. Unlike classical algorithms, RLALIGN is incognizant to the nature of the scoring scheme, leading to easy generalization to a variety of problem variants.
多序列比对(MSA)是生物信息学中研究得最好的问题之一,因为广泛的基因组学、蛋白质组学和进化分析都依赖于它。然而问题是np困难,现有的启发式是不完善的。强化学习(RL)技术最近作为解决各种计算问题的潜在解决方案而出现,但尚未应用于MSA。在本文中,我们描述了一种使用强化学习来解决MSA问题的方法RLALIGN。RLALIGN基于异步优势Actor批评家(A3C),这是一个前沿的RL框架。然而,由于缺乏目标状态,它需要进行一些重要的修改。RLALIGN可以训练成精确地对齐中等长度的序列,各种启发式方法允许它扩展到更长的序列。所产生的对齐精度与已建立的对齐算法相当,并且通常优于这些算法。总的来说,我们的工作证明了强化学习方法在复杂组合问题(如MSA)中的潜力。RLALIGN将被证明对重新排列任务很有用,其中需要对较大对齐的部分进行优化。与经典算法不同的是,RLALIGN无法识别评分方案的本质,因此很容易泛化到各种问题变体。
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引用次数: 8
[Regular Paper] A High-Performance Sequence Analysis Engine for Shotgun Metagenomics through GPU Acceleration 基于GPU加速的Shotgun Metagenomics的高性能序列分析引擎
Ying-Feng Hsu, Morito Matsuoka, Nicolas Jung, Y. Matsumoto, D. Motooka, S. Nakamura
With the continual growth of low-cost and high-throughput DNA sequence technology, the scale and amount of next-generation sequencing (NGS) datasets are continually increasing in many genomics research areas. Shotgun metagenomics sequencing provides comprehensive information on microorganisms, based on complex samples of the ecosystem. Due to challenges of its scale and computational complexity, efficient sequence processing and analyzing tools are needed. In this paper, we propose a novel high-performance shotgun metagenomics sequence analysis engine for the task of sequence comparison. It includes two major components. First, a customized shifting database, which is optimized from any existing DNA sequence dataset. Second, a high-performance sequence computation algorithm that utilizes the customized shifting reference database and accelerates GPU parallel computing. We elaborated upon the efficiency and computational complexity of our proposed approach in an HPC server, which has eight Nvidia Tesla P100 GPUs. We also conducted a case study to detect viral sequences from patients' blood samples. Our experimental result shows that we obtain similar accuracy to the conventional BLAST method, but with a computational speed that is about twenty times faster.
随着低成本、高通量DNA测序技术的不断发展,下一代测序(NGS)数据集的规模和数量在许多基因组学研究领域不断增加。霰弹枪宏基因组测序基于生态系统的复杂样本,提供了关于微生物的全面信息。由于其规模和计算复杂度的挑战,需要高效的序列处理和分析工具。本文提出了一种新型的高性能霰弹枪宏基因组序列分析引擎,用于序列比较。它包括两个主要组成部分。首先,根据现有的DNA序列数据集进行优化,建立自定义的移位数据库。其次,利用自定义移位参考数据库加速GPU并行计算的高性能序列计算算法。我们在HPC服务器上详细阐述了我们提出的方法的效率和计算复杂性,该服务器具有8个Nvidia Tesla P100 gpu。我们还进行了一个病例研究,从患者血液样本中检测病毒序列。我们的实验结果表明,我们获得了与传统BLAST方法相似的精度,但计算速度快了大约20倍。
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引用次数: 0
Mutation Analysis of Second Primary Tumors in the Head and Neck Cancer by Next Generation Sequencing 应用下一代测序技术分析头颈癌第二原发肿瘤的突变
Ting-Yuan Liu, Chien-Chin Lee, Hsi-Yuan Huang, Jan-Gowth Chang
More than 90% of malignant tumors in the head and neck are squamous carcinomas. These patients are with an average survival rate of about 5 years. However, some of the head and neck cancer(HNC) patients had the poor survival rate because of development of second primary tumors. In this study, the sequencing was performed using the Illumina system and Sanger sequencing was used to validate all identified mutations. We analyzed primary and second primary tumors in HNC and identified 23 mutant verification only in second primary tumors; 32 mutant verification only in primary tumors; 38 mutant verification in both of them. This mutant verification only in second primary tumors might be the cause of the second primary oral cancer.
头颈部90%以上的恶性肿瘤为鳞状癌。这些患者的平均存活率约为5年。然而,一些头颈癌(HNC)患者由于第二原发肿瘤的发展,生存率较低。在本研究中,测序使用Illumina系统,并使用Sanger测序来验证所有鉴定的突变。我们分析了HNC的原发和第二原发肿瘤,仅在第二原发肿瘤中鉴定了23个突变体;仅在原发肿瘤中验证32个突变体;两个都有38个突变体。这种仅在第二原发肿瘤中证实的突变可能是导致第二原发口腔癌的原因。
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引用次数: 0
[Regular Paper] Detection of H. pylori Induced Gastric Inflammation by Diffuse Reflectance Analysis 漫反射分析法检测幽门螺杆菌性胃炎
Alexandre Krebs, V. Camilo, E. Touati, Y. Benezeth, V. Michel, G. Jouvion, Fan Yang, D. Lamarque, F. Marzani
Spectral acquisitions contain rich information and thus, are promising modalities for early detection of gastric diseases. In this study, we analyze the diffuse reflectance of the gastric inflammatory lesions induced by the bacterium H. pylori in the mouse stomach. A pipeline has been designed to characterize and classify spectra acquired on mice. The pipeline is based on a band clustering algorithm followed by the computation of meaningful division and subtraction features and by classification with a linear SVM classifier. Currently, the pipeline is able to recognize inflamed stomach's spectra with an accuracy of 98%. These results are promising and the same pipeline could be adapted for the study of gastric pathologies in humans.
光谱采集包含丰富的信息,因此是早期发现胃部疾病的有希望的方式。在这项研究中,我们分析了幽门螺杆菌在小鼠胃中引起的胃炎性病变的漫反射。设计了一个管道来表征和分类在小鼠身上获得的光谱。该管道基于带聚类算法,然后计算有意义的除法和减法特征,并使用线性支持向量机分类器进行分类。目前,该管道能够以98%的准确率识别炎症胃的光谱。这些结果是有希望的,同样的管道可以适用于人类胃病理的研究。
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引用次数: 1
Psycho-Physiological Changes Depend on Differences in the Presentation Ratio of Non-target Stimuli 心理生理变化取决于非目标刺激呈现比例的差异
Hiroaki Yoshikawa, H. Hagiwara
The purpose of this study was to examine features of attention and concentration based on differences in the amount of unnecessary information using multiple psycho-physiological evaluations. We used the Roken Arousal Scale as a subjective evaluation, and electroencephalograms (alpha attenuation coefficient (AAC), P300) and near-infrared spectroscopy (oxygenated hemoglobin) as physiological indices. To investigate the psycho-physiological differences due to differences in the amount of unnecessary information, we used the oddball paradigm task. As the number of non-target stimuli increased, the oxygenated hemoglobin concentration increased and the P300 amplitude and AAC value tended to decrease. In conclusion, when the amount of unnecessary information is small, the load on the brain and arousal level of decrease are suppressed, and work can be performed while maintaining attention and concentration.
本研究的目的是使用多种心理生理评估来检查基于不必要信息数量差异的注意和集中的特征。我们采用Roken唤醒量表作为主观评价,脑电图(α衰减系数(AAC), P300)和近红外光谱(氧合血红蛋白)作为生理指标。为了研究由于不必要信息数量的差异而导致的心理生理差异,我们使用了古怪范式任务。随着非目标刺激次数的增加,氧合血红蛋白浓度升高,P300振幅和AAC值有降低的趋势。综上所述,当不必要的信息量较小时,大脑的负荷和觉醒水平的降低受到抑制,可以在保持注意力集中的情况下进行工作。
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引用次数: 0
期刊
2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE)
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